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662  structures 1819  species 0  interactions 38689  sequences 778  architectures

Family: Y_phosphatase (PF00102)

Summary: Protein-tyrosine phosphatase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Protein tyrosine phosphatase". More...

Protein tyrosine phosphatase Edit Wikipedia article

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Protein-tyrosine phosphatase Provide feedback

No Pfam abstract.

Literature references

  1. Hof P, Pluskey S, Dhe-Paganon S, Eck MJ, Shoelson SE; , Cell 1998;92:441-450.: Crystal structure of the tyrosine phosphatase SHP-2. PUBMED:9491886 EPMC:9491886


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000242

Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC ) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [ PUBMED:9818190 , PUBMED:14625689 ]. The PTP superfamily can be divided into four subfamilies [ PUBMED:12678841 ]:

  • (1) pTyr-specific phosphatases
  • (2) dual specificity phosphatases (dTyr and dSer/dThr)
  • (3) Cdc25 phosphatases (dTyr and/or dThr)
  • (4) LMW (low molecular weight) phosphatases

Based on their cellular localisation, PTPases are also classified as:

  • Receptor-like, which are transmembrane receptors that contain PTPase domains [ PUBMED:16672235 ]
  • Non-receptor (intracellular) PTPases [ PUBMED:8948575 ]

All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif [ PUBMED:9646865 ]. Functional diversity between PTPases is endowed by regulatory domains and subunits.

This entry represents the PTPase domain found in several tyrosine-specific protein phosphatases (PTPases).

Structurally, all known receptor PTPases, are made up of a variable length extracellular domain, followed by a transmembrane region and a C-terminal catalytic cytoplasmic domain. Some of the receptor PTPases contain fibronectin type III (FN-III) repeats, immunoglobulin-like domains, MAM domains or carbonic anhydrase-like domains in their extracellular region. The cytoplasmic region generally contains two copies of the PTPase domain. The first seems to have enzymatic activity, while the second is inactive. The inactive domains of tandem phosphatases can be divided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre [ PUBMED:14739250 ]. PTPase domains consist of about 300 amino acids. There are two conserved cysteines, the second one has been shown to be absolutely required for activity. Furthermore, a number of conserved residues in its immediate vicinity have also been shown to be important.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Phosphatase (CL0031), which has the following description:

This family includes tyrosine and dual specificity phosphatase enzymes.

The clan contains the following 16 members:

CDKN3 DSPc DSPn DUF442 Init_tRNA_PT LMWPc Myotub-related NleF_casp_inhib PTPlike_phytase PTS_IIB Rhodanese Ssu72 Syja_N Y_phosphatase Y_phosphatase2 Y_phosphatase3

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(91)
Full
(38689)
Representative proteomes UniProt
(71549)
RP15
(6927)
RP35
(15659)
RP55
(34896)
RP75
(46441)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(91)
Full
(38689)
Representative proteomes UniProt
(71549)
RP15
(6927)
RP35
(15659)
RP55
(34896)
RP75
(46441)
Alignment:
Format:
Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(91)
Full
(38689)
Representative proteomes UniProt
(71549)
RP15
(6927)
RP35
(15659)
RP55
(34896)
RP75
(46441)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Swissprot_feature_table
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 91
Number in full: 38689
Average length of the domain: 209.20 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 31.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 235
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Selections

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Y_phosphatase domain has been found. There are 662 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JXZ9 View 3D Structure Click here
A0A0G2K2N0 View 3D Structure Click here
A0A0G2K2W0 View 3D Structure Click here
A0A0G2K754 View 3D Structure Click here
A0A0G2KFA2 View 3D Structure Click here
A0A0H2UKT5 View 3D Structure Click here
A0A0H2UKT5 View 3D Structure Click here
A0A0R0ENX4 View 3D Structure Click here
A0A0R4I9I3 View 3D Structure Click here
A0A0R4I9I3 View 3D Structure Click here
A0A0R4IER5 View 3D Structure Click here
A0A0R4IPR0 View 3D Structure Click here
A0A0R4ITJ9 View 3D Structure Click here
A0A1B1LZI1 View 3D Structure Click here
A0A1B1LZI1 View 3D Structure Click here
A0A1D6EHC5 View 3D Structure Click here
A0A1D6MYT0 View 3D Structure Click here
A0A1D6MYT0 View 3D Structure Click here
A0A1D8PLX9 View 3D Structure Click here
A0A1D8PU75 View 3D Structure Click here
A0A1L1QZV5 View 3D Structure Click here
A0A286Y7Z0 View 3D Structure Click here
A0A286Y7Z0 View 3D Structure Click here
A0A286Y832 View 3D Structure Click here
A0A286Y832 View 3D Structure Click here
A0A286YB50 View 3D Structure Click here
A0A286YB50 View 3D Structure Click here
A0A286YBL8 View 3D Structure Click here
A0A2R8Q2T0 View 3D Structure Click here
A0A2R8Q7H4 View 3D Structure Click here
A0A2R8QCZ8 View 3D Structure Click here
A0A2R8QCZ8 View 3D Structure Click here
A0A2R8QL35 View 3D Structure Click here
A0A2R8QLE2 View 3D Structure Click here
A0A2R8QLE2 View 3D Structure Click here
A0A2R8RL72 View 3D Structure Click here
A0A2R8RLA8 View 3D Structure Click here
A0A2R8RLA8 View 3D Structure Click here
A1L1L3 View 3D Structure Click here
A1ZAB3 View 3D Structure Click here
A2A8L5 View 3D Structure Click here
A2A8L5 View 3D Structure Click here
A2ALK8 View 3D Structure Click here
A3KPJ4 View 3D Structure Click here
A4HWS2 View 3D Structure Click here
A4HWS4 View 3D Structure Click here
A4IDJ2 View 3D Structure Click here
A4IDV1 View 3D Structure Click here
A4IFW2 View 3D Structure Click here
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A5I9F0 View 3D Structure Click here
A5I9F0 View 3D Structure Click here
A8DZA4 View 3D Structure Click here
B0K032 View 3D Structure Click here
B0UYE7 View 3D Structure Click here
B0V2N1 View 3D Structure Click here
B0V2N1 View 3D Structure Click here
B1AUH1 View 3D Structure Click here
B1AUH1 View 3D Structure Click here
B2GV87 View 3D Structure Click here
B2GV87 View 3D Structure Click here
B2RU80 View 3D Structure Click here
B3DK56 View 3D Structure Click here
B3DK56 View 3D Structure Click here
B6HY54 View 3D Structure Click here
B8A5J5 View 3D Structure Click here
B8A5J5 View 3D Structure Click here
B9EKR1 View 3D Structure Click here
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C3JXD8 View 3D Structure Click here
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E7F716 View 3D Structure Click here
E7FA22 View 3D Structure Click here
E7FC59 View 3D Structure Click here
E9Q0N2 View 3D Structure Click here
E9Q612 View 3D Structure Click here
F1LP13 View 3D Structure Click here
F1LP13 View 3D Structure Click here
F1LPJ1 View 3D Structure Click here
F1LPJ1 View 3D Structure Click here
F1LQQ5 View 3D Structure Click here
F1LXJ9 View 3D Structure Click here
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F1M8E7 View 3D Structure Click here
F1MAG7 View 3D Structure Click here
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F1Q653 View 3D Structure Click here
F1Q8I4 View 3D Structure Click here
F1QBE0 View 3D Structure Click here
F1QDL0 View 3D Structure Click here
F1QE38 View 3D Structure Click here
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F1QFY3 View 3D Structure Click here
F1QIX3 View 3D Structure Click here
F1QJW2 View 3D Structure Click here
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F1QLN8 View 3D Structure Click here
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F1QWY5 View 3D Structure Click here
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F1QZX7 View 3D Structure Click here
F1QZX7 View 3D Structure Click here
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F1R8P8 View 3D Structure Click here
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G5EC24 View 3D Structure Click here
G5EC69 View 3D Structure Click here
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G5EG43 View 3D Structure Click here
G5EGA9 View 3D Structure Click here
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G5EGJ9 View 3D Structure Click here
G5EGU2 View 3D Structure Click here
G8JZG5 View 3D Structure Click here
H2KZM6 View 3D Structure Click here
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I1LD92 View 3D Structure Click here
K7N422 View 3D Structure Click here
M0RB22 View 3D Structure Click here
M0RB22 View 3D Structure Click here
O01435 View 3D Structure Click here
O01508 View 3D Structure Click here
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O01555 View 3D Structure Click here
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O01736 View 3D Structure Click here
O01767 View 3D Structure Click here
O01777 View 3D Structure Click here
O01913 View 3D Structure Click here
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O08617 View 3D Structure Click here
O14522 View 3D Structure Click here
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O16728 View 3D Structure Click here
O17840 View 3D Structure Click here
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O44136 View 3D Structure Click here
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O55082 View 3D Structure Click here
O61722 View 3D Structure Click here
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O70274 View 3D Structure Click here
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P04157 View 3D Structure Click here
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P06800 View 3D Structure Click here
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P25044 View 3D Structure Click here
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P40048 View 3D Structure Click here
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P41499 View 3D Structure Click here
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P43378 View 3D Structure Click here
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P54637 View 3D Structure Click here
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P70289 View 3D Structure Click here
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P80560 View 3D Structure Click here
P81718 View 3D Structure Click here
P91147 View 3D Structure Click here
P91179 View 3D Structure Click here
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P91568 View 3D Structure Click here
Q03348 View 3D Structure Click here
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Q0IU77 View 3D Structure Click here
Q0KI81 View 3D Structure Click here
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Q16825 View 3D Structure Click here
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Q18301 View 3D Structure Click here
Q18385 View 3D Structure Click here
Q18415 View 3D Structure Click here
Q18652 View 3D Structure Click here
Q1MTF9 View 3D Structure Click here
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Q20019 View 3D Structure Click here
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Q20108 View 3D Structure Click here
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Q2QX07 View 3D Structure Click here
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Q4CT10 View 3D Structure Click here
Q4CUJ8 View 3D Structure Click here
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Q4DCU3 View 3D Structure Click here
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Q4DPP2 View 3D Structure Click here
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Q54CH3 View 3D Structure Click here
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Q63259 View 3D Structure Click here
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Q641Z2 View 3D Structure Click here
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Q64612 View 3D Structure Click here
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Q6P9X4 View 3D Structure Click here
Q6PB44 View 3D Structure Click here
Q6TGR5 View 3D Structure Click here
Q7KMQ6 View 3D Structure Click here
Q7YWN5 View 3D Structure Click here
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Q803R3 View 3D Structure Click here
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Q8MYN1 View 3D Structure Click here
Q92729 View 3D Structure Click here
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Q95XJ2 View 3D Structure Click here
Q95XL1 View 3D Structure Click here
Q95Y26 View 3D Structure Click here
Q966M2 View 3D Structure Click here
Q99952 View 3D Structure Click here
Q99M80 View 3D Structure Click here
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